April 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 84af64: Cgroup metric plugin: attempt to deal with multili...
by GitHub 30 Apr '18

30 Apr '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 84af648f017dad95871bb43b65e8d860391066c8 https://github.com/galaxyproject/galaxy/commit/84af648f017dad95871bb43b65e8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/util/__init__.py Log Message: ----------- Cgroup metric plugin: attempt to deal with multiline params, and store numeric values in the numeric table. Also fix a display bug. Commit: 3ee40bfe53088b57da6b3a44efd5ac835ec6f1e7 https://github.com/galaxyproject/galaxy/commit/3ee40bfe53088b57da6b3a44efd5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #5989 from natefoo/cgroup-metric-fixes [18.05] Fixes for the Cgroup metric plugin Compare: https://github.com/galaxyproject/galaxy/compare/916078beb0b5...3ee40bfe5308

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[galaxyproject/galaxy] f50715: Remove __global__
by GitHub 30 Apr '18

30 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f50715df8377af74afce2231aa857a98684f6868 https://github.com/galaxyproject/galaxy/commit/f50715df8377af74afce2231aa85… Author: E Rasche <hxr(a)hx42.org> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/statsd.py Log Message: ----------- Remove __global__ Commit: 8c152bda45cbf3b49610a9933bd6c38f1724942a https://github.com/galaxyproject/galaxy/commit/8c152bda45cbf3b49610a9933bd6… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/statsd.py Log Message: ----------- Merge pull request #6011 from erasche/remove_global Remove duplicate metric sending Compare: https://github.com/galaxyproject/galaxy/compare/c2ee91508bcc...8c152bda45cb

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[galaxyproject/galaxy] 717e11: enable testing for more BAM types
by GitHub 30 Apr '18

30 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 717e1104c1e32f79b84de6ffbc481b105087f17f https://github.com/galaxyproject/galaxy/commit/717e1104c1e32f79b84de6ffbc48… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-04-28 (Sat, 28 Apr 2018) Changed paths: M lib/galaxy/tools/verify/__init__.py Log Message: ----------- enable testing for more BAM types Commit: abf23cdc0bb22542577e5ddefac38242c9ddf8ee https://github.com/galaxyproject/galaxy/commit/abf23cdc0bb22542577e5ddefac3… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/tools/verify/__init__.py Log Message: ----------- Merge pull request #6010 from bgruening/test_bam_subtypes [18.01] enable testing for more BAM types Compare: https://github.com/galaxyproject/galaxy/compare/103cb51ec368...abf23cdc0bb2

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[galaxyproject/infrastructure-playbook] f4186c: Install Data::Dumper perl module on nodes for olde...
by GitHub 28 Apr '18

28 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: f4186c1ab8ea0414a875247bfe59d9aa84bd6f9e https://github.com/galaxyproject/infrastructure-playbook/commit/f4186c1ab8e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-28 (Sat, 28 Apr 2018) Changed paths: M env/tacc/group_vars/galaxynodes.yml Log Message: ----------- Install Data::Dumper perl module on nodes for older tools

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[galaxyproject/galaxy] 0875b8: fix bowtie2 link
by GitHub 28 Apr '18

28 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0875b8e65d6d5d7130c829ec8e5b7f9bffcced3a https://github.com/galaxyproject/galaxy/commit/0875b8e65d6d5d7130c829ec8e5b… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-04-28 (Sat, 28 Apr 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- fix bowtie2 link Commit: c2ee91508bcc96cadfd7b23fba8a8d60e6f5547a https://github.com/galaxyproject/galaxy/commit/c2ee91508bcc96cadfd7b23fba8a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-28 (Sat, 28 Apr 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6009 from galaxyproject/bowtie2_link fix bowtie2 link Compare: https://github.com/galaxyproject/galaxy/compare/acc988981546...c2ee91508bcc

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[galaxyproject/galaxy] 0875b8: fix bowtie2 link
by GitHub 28 Apr '18

28 Apr '18

Branch: refs/heads/bowtie2_link Home: https://github.com/galaxyproject/galaxy Commit: 0875b8e65d6d5d7130c829ec8e5b7f9bffcced3a https://github.com/galaxyproject/galaxy/commit/0875b8e65d6d5d7130c829ec8e5b… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-04-28 (Sat, 28 Apr 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- fix bowtie2 link

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[galaxyproject/usegalaxy-playbook] ebf920: Add nate01.galaxyproject.org for testing
by GitHub 27 Apr '18

27 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ebf9208ccccac690a9f73ba3691b682ebf726845 https://github.com/galaxyproject/usegalaxy-playbook/commit/ebf9208ccccac690… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M env/test/group_vars/dbservers/vault.yml M env/test/group_vars/webservers/vars.yml A env/test/templates/nginx/nate01.j2 Log Message: ----------- Add nate01.galaxyproject.org for testing

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[galaxyproject/usegalaxy-playbook] 33db7b: Update common roles for bug
by GitHub 27 Apr '18

27 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 33db7b7b9aea291f1bede9b3df43eba4ba11f27b https://github.com/galaxyproject/usegalaxy-playbook/commit/33db7b7b9aea291f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M common_roles Log Message: ----------- Update common roles for bug

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[galaxyproject/infrastructure-playbook] 660f95: Update common roles for bug
by GitHub 27 Apr '18

27 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 660f95dc945e1ed1638b873d89a776d5f8f23c88 https://github.com/galaxyproject/infrastructure-playbook/commit/660f95dc945… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M common_roles Log Message: ----------- Update common roles for bug

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[galaxyproject/usegalaxy-playbook] 29b557: Update common roles and update for crontabs inheri...
by GitHub 27 Apr '18

27 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 29b55788c132b7da81fbaf0e64585c29968e5f98 https://github.com/galaxyproject/usegalaxy-playbook/commit/29b55788c132b7da… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M common_roles M env/main/host_vars/galaxy-web-05.tacc.utexas.edu.yml M env/test/host_vars/galaxy07.tacc.utexas.edu.yml M env/testtoolshed/group_vars/toolshedservers/vars.yml M env/toolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update common roles and update for crontabs inheritance chain

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